Job ID = 4178557 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,035,433 reads read : 30,070,866 reads written : 15,035,433 reads 0-length : 15,035,433 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:21 15035433 reads; of these: 15035433 (100.00%) were unpaired; of these: 3300702 (21.95%) aligned 0 times 9847078 (65.49%) aligned exactly 1 time 1887653 (12.55%) aligned >1 times 78.05% overall alignment rate Time searching: 00:03:21 Overall time: 00:03:21 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 7318670 / 11734731 = 0.6237 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:12:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827829/SRX5827829.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827829/SRX5827829.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827829/SRX5827829.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827829/SRX5827829.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 05 Dec 2019 13:12:36: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:12:36: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:12:43: 1000000 INFO @ Thu, 05 Dec 2019 13:12:50: 2000000 INFO @ Thu, 05 Dec 2019 13:12:58: 3000000 INFO @ Thu, 05 Dec 2019 13:13:05: 4000000 INFO @ Thu, 05 Dec 2019 13:13:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827829/SRX5827829.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827829/SRX5827829.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827829/SRX5827829.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827829/SRX5827829.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 05 Dec 2019 13:13:06: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:13:06: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:13:08: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:13:08: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:13:08: #1 total tags in treatment: 4416061 INFO @ Thu, 05 Dec 2019 13:13:08: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:13:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:13:08: #1 tags after filtering in treatment: 4416061 INFO @ Thu, 05 Dec 2019 13:13:08: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:13:08: #1 finished! INFO @ Thu, 05 Dec 2019 13:13:08: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:13:08: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:13:08: #2 number of paired peaks: 808 WARNING @ Thu, 05 Dec 2019 13:13:08: Fewer paired peaks (808) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 808 pairs to build model! INFO @ Thu, 05 Dec 2019 13:13:08: start model_add_line... INFO @ Thu, 05 Dec 2019 13:13:08: start X-correlation... INFO @ Thu, 05 Dec 2019 13:13:08: end of X-cor INFO @ Thu, 05 Dec 2019 13:13:08: #2 finished! INFO @ Thu, 05 Dec 2019 13:13:08: #2 predicted fragment length is 134 bps INFO @ Thu, 05 Dec 2019 13:13:08: #2 alternative fragment length(s) may be 134 bps INFO @ Thu, 05 Dec 2019 13:13:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827829/SRX5827829.05_model.r INFO @ Thu, 05 Dec 2019 13:13:08: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:13:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:13:13: 1000000 INFO @ Thu, 05 Dec 2019 13:13:17: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:13:19: 2000000 INFO @ Thu, 05 Dec 2019 13:13:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827829/SRX5827829.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:13:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827829/SRX5827829.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:13:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827829/SRX5827829.05_summits.bed INFO @ Thu, 05 Dec 2019 13:13:23: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2445 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:13:26: 3000000 INFO @ Thu, 05 Dec 2019 13:13:33: 4000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:13:35: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:13:35: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:13:35: #1 total tags in treatment: 4416061 INFO @ Thu, 05 Dec 2019 13:13:35: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:13:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:13:35: #1 tags after filtering in treatment: 4416061 INFO @ Thu, 05 Dec 2019 13:13:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:13:35: #1 finished! INFO @ Thu, 05 Dec 2019 13:13:35: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:13:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:13:36: #2 number of paired peaks: 808 WARNING @ Thu, 05 Dec 2019 13:13:36: Fewer paired peaks (808) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 808 pairs to build model! INFO @ Thu, 05 Dec 2019 13:13:36: start model_add_line... INFO @ Thu, 05 Dec 2019 13:13:36: start X-correlation... INFO @ Thu, 05 Dec 2019 13:13:36: end of X-cor INFO @ Thu, 05 Dec 2019 13:13:36: #2 finished! INFO @ Thu, 05 Dec 2019 13:13:36: #2 predicted fragment length is 134 bps INFO @ Thu, 05 Dec 2019 13:13:36: #2 alternative fragment length(s) may be 134 bps INFO @ Thu, 05 Dec 2019 13:13:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827829/SRX5827829.10_model.r INFO @ Thu, 05 Dec 2019 13:13:36: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:13:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:13:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827829/SRX5827829.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827829/SRX5827829.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827829/SRX5827829.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827829/SRX5827829.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 05 Dec 2019 13:13:36: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:13:36: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:13:43: 1000000 INFO @ Thu, 05 Dec 2019 13:13:45: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:13:50: 2000000 INFO @ Thu, 05 Dec 2019 13:13:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827829/SRX5827829.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:13:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827829/SRX5827829.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:13:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827829/SRX5827829.10_summits.bed INFO @ Thu, 05 Dec 2019 13:13:50: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1318 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:13:57: 3000000 INFO @ Thu, 05 Dec 2019 13:14:04: 4000000 INFO @ Thu, 05 Dec 2019 13:14:07: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:14:07: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:14:07: #1 total tags in treatment: 4416061 INFO @ Thu, 05 Dec 2019 13:14:07: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:14:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:14:07: #1 tags after filtering in treatment: 4416061 INFO @ Thu, 05 Dec 2019 13:14:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:14:07: #1 finished! INFO @ Thu, 05 Dec 2019 13:14:07: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:14:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:14:07: #2 number of paired peaks: 808 WARNING @ Thu, 05 Dec 2019 13:14:07: Fewer paired peaks (808) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 808 pairs to build model! INFO @ Thu, 05 Dec 2019 13:14:07: start model_add_line... INFO @ Thu, 05 Dec 2019 13:14:07: start X-correlation... INFO @ Thu, 05 Dec 2019 13:14:07: end of X-cor INFO @ Thu, 05 Dec 2019 13:14:07: #2 finished! INFO @ Thu, 05 Dec 2019 13:14:07: #2 predicted fragment length is 134 bps INFO @ Thu, 05 Dec 2019 13:14:07: #2 alternative fragment length(s) may be 134 bps INFO @ Thu, 05 Dec 2019 13:14:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827829/SRX5827829.20_model.r INFO @ Thu, 05 Dec 2019 13:14:11: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:14:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:14:19: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:14:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827829/SRX5827829.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:14:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827829/SRX5827829.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:14:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827829/SRX5827829.20_summits.bed INFO @ Thu, 05 Dec 2019 13:14:25: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (559 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。